User: jevanveen

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jevanveen20
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2 years, 3 months ago
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j********@alum.mit.edu

Posts by jevanveen

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Looking for perspective on a odd MA plot / skewed data
... This is helpful information... I have a decent amount of experience with R, but I did my first seq analyses on galaxy, and so... if it aint broke, don't fix it, right? Well, I guess now it's broke, lol. Will give it a shot. Cheers ...
written 6 months ago by jevanveen20
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Comment: C: Looking for perspective on a odd MA plot / skewed data
... Thanks for responding! Replicates are 3 in one condition, 4 in the other. Sorry, do you mean MA-plot with non-shrunken LFC values? I am still running my alignments and DESeq on usegalaxy. As far as I can tell, the LFC values are not shrunken by default. ...
written 6 months ago by jevanveen20
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Looking for perspective on a odd MA plot / skewed data
... Hello Biostars! I (and collaborators) recently performed a patch-seq experiment... That is, we did patch-clamp recording of neuronal firing, then aspirated the contents of recorded cells, and made RNA seq compatible libraries. Data look alright - certainly there is a lot of PCR duplication. Pro ...
patch-seq rna-seq written 6 months ago by jevanveen20 • updated 5 months ago by Biostar ♦♦ 20
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Comment: C: Bonferroni multiple corrections question
... This is fantastically helpful and straight to the point. Thank you very much!!! ...
written 9 months ago by jevanveen20
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Bonferroni multiple corrections question
... Hello Biostars! I have been analyzing some single cell RNA sequencing data, which compares neural transcriptomes from mice treated with either vehicle, or a drug. All the basic stuff is going fine. When I get my clusters, I find not many *super* interesting significant drug induced DEGs. If I do ...
scrna-seq rna-seq gsea statistics written 9 months ago by jevanveen20 • updated 9 months ago by dsull1.4k
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Comment: C: Single cell RNA-seq guided correlation analysis
... Hey I know much time has passed, but I went with your suggestion #1, it looked great, and now it is part of my published work: https://elifesciences.org/articles/43668 so thank you very much again! Ed ...
written 9 months ago by jevanveen20
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QC before single cell RNA seq?
... Background: We have done single cell RNA seq, it went well, and we are preparing to do more projects. When we did it the first time, we troubleshot our cell dissociation protocol and made sure that we could get good RINs from bulk RNA before proceeding. Now we are dealing with projects that have f ...
qc rna-seq single cell written 2.1 years ago by jevanveen20
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Comment: C: Single cell RNA-seq guided correlation analysis
... Thank you - very helpful insights ...
written 2.2 years ago by jevanveen20
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Comment: C: Single cell RNA-seq guided correlation analysis
... Thank you - I was playing with WGCNA a bit before posting this, but it seems to do whole transcriptome clustering, whereas I want to specifically start with an a priori list that I took from an scRNA seq paper to asses coordinate regulation of cell differentiation state. It kind of sounds like this ...
written 2.3 years ago by jevanveen20
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Answer: A: How to analyse RNA-Seq data with JUST geneID and TPM values
... DESeq2 is probably what you want. It does a fine job of giving you DE genes starting with TPM values generated by Kallisto or Salmon. There's a user friendly interface available (free) at usegalazy.org ...
written 2.3 years ago by jevanveen20

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Popular Question 22 months ago, created a question with more than 1,000 views. For Single cell RNA-seq guided correlation analysis

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